I have developed games for NES, Game Boy, and Game Boy Advance, and have dabbled with Super NES. Now I'm beginning to learn Genesis programming, and eventually, I may consider developing games for distribution on cartridge.

My PC runs Xubuntu 18.04, a distribution of GNU/Linux. I chose it in part because I found it faster to boot and faster to start applications than Windows. When I looked for a debugging Genesis emulator compatible with Ubuntu, I first looked at the Tools page on SpritesMind. Its recommended "Gens KMod" emulator shows a screenshot with a 2003 copyright date. Gens was reportedly the source of much of FCEUX's debugging UI, but it appears to be no longer maintained.

Elsewhere I saw someone recommend Regen. Despite its being proprietary software (and thus unethical software by the definition of some members of this forum), I decided to evaluate it. But I hit a snag when I read the included README file:

======================
Regen/GTK+ 0.95 ReadMe
======================

By AamirM, Copyright (C) 2009

The build on the website is ten years old, making me fear NESticle/Genecyst-class accuracy. But this struck me as worse:

You may use and/or redistribute Regen provided that you :

1) Do not modify and/or alter, in any way, the files included.
2) You distribute all the files you got originally with Regen.
3) You may not sell, lease, rent or otherwise seek to gain monetary profit from
Regen.
4) You may not distribute Regen with ROM images unless you have the legal right
to distribute them.
5) You may not use Regen for commercial purposes.

The README file does not rigorously define "commercial purposes." However, the license of a different emulator-like software package, the Oracle VirtualBox Extension Pack Personal Use and Evaluation License, defines noncommercial use to "expressly exclude any use of the Product for commercial purposes or to operate, run, or act on behalf of or for the benefit of a business, organization, governmental organization, or educational institution." If Regen's definition of commercial use remotely matches Oracle's, this would rule out using Regen to test a Genesis-compatible program being developed with the intent of eventually distributing copies of the Genesis-compatible program on cartridge for a fee.

Gens KMod is a fork from Gens, whose last version was released by the year you mention. KMod however has been last updated on 2015, but only shows half the VRAM. I edited it myself to show the full memory and posted the fixed executable, but some people claim it contains virus (I wonder how? I'm not THAT kind of evil, my PC is clean (last checked June 2nd), but I used a pirate copy of Visual Studio 2010 to build that; not sure if had anything to do, but if you aim to edit it yourself it's fairly easy)

And honestly? KMod could have choppy framerate, not-so-good sound emulation (but better than Regen), timings that are slightly off, no Address Error emulation BUT, IMHO is actually fairly nice for debugging, at least better than Regen. You can debug hardware flags, plane maps and sprite list, all memories (and even disassemble ROM or MCD's PRAM) while your program keeps running. MD RAM watchers are fairly useful for static variables, and there was an "easy way" to export watchers from programs built with SGDK, but I don't know details. There's a built-in console if you'd like to export messages from the game's side, and supports GDB.
KMod is NOT the best emulator to test your final work but, at least is good enough to debug code logic and I found it's been easier to fix bugs with it. Once I'm happy with what I have I run a final test on BlastEm, and after a good bunch of coding, I send a ROM to a friend to test on his hardware